http://2013.igem.org/wiki/index.php?title=Team:Dundee/Project/NetlogoSec&feed=atom&action=historyTeam:Dundee/Project/NetlogoSec - Revision history2024-03-28T22:02:06ZRevision history for this page on the wikiMediaWiki 1.16.5http://2013.igem.org/wiki/index.php?title=Team:Dundee/Project/NetlogoSec&diff=282610&oldid=prevKyleharrison at 20:08, 3 October 20132013-10-03T20:08:03Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> archive="NetLogoLite.jar"</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> archive="NetLogoLite.jar"</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <param name="DefaultModel"</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <param name="DefaultModel"</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> value="SECGATEcommented.nlogo"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> value="SECGATEcommented.nlogo"></div></td></tr>
</table>Kyleharrisonhttp://2013.igem.org/wiki/index.php?title=Team:Dundee/Project/NetlogoSec&diff=266516&oldid=prevJHAllan at 12:05, 2 October 20132013-10-02T12:05:41Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <!-- Title --></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <!-- Title --></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <div class="page-header"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <div class="page-header"></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <h2><b>NetLogo </b> - SECGATE <del class="diffchange diffchange-inline">Transportation</del></h2></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <h2><b>NetLogo </b> - SECGATE <ins class="diffchange diffchange-inline">Transport</ins></h2></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p style="text-align:justify"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <p style="text-align:justify"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> The applet requires Java 5 or higher. Java must be enabled in your browser settings. Mac users must have Mac OS X 10.4 or higher. Windows and Linux users may obtain the latest Java from Oracle's Java site.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> The applet requires Java 5 or higher. Java must be enabled in your browser settings. Mac users must have Mac OS X 10.4 or higher. Windows and Linux users may obtain the latest Java from Oracle's Java site.</div></td></tr>
</table>JHAllanhttp://2013.igem.org/wiki/index.php?title=Team:Dundee/Project/NetlogoSec&diff=258931&oldid=prevKyleharrison at 11:29, 1 October 20132013-10-01T11:29:51Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"> <div class="row" ></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"> <div class="span12"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"> <h2>WHAT IS IT?</h2></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"> <p style="text-align:justify"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"> This model follows on the Simple Kinetics 2 model. In Simple Kinetics 2, we saw how changes to variables such as temperature, volume, and concentration affected the rate at which a chemical reaction reached an equilibrium state. Here we model the same phenomenon based upon a physical separation.</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"> This model investigates some laboratory methods that chemists use to purify chemicals. Most of these methods are based upon physical properties of molecular separation. The same principles that affect chemical equilibrium affect physical equilibrium as well. By changing the variables of temperature, volume, and concentration, we can affect not only the speed at which a system reaches equilibrium, but also the nature of the distribution ratio. In this model, we watch how these factors affect the physical distribution of red molecules that are considered “dissolved” in a blue solvent.</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"> </p></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"> <h2>HOW TO USE IT</h2></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"> <p style="text-align:justify"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"> Setup the model by pressing either the SETUP-RANDOM or the SETUP-SIDE buttons at the top of the Interface tab. SETUP-RANDOM distributes all the molecules randomly around the world. SETUP-SIDE distributes the blue molecules evenly, while placing the red molecules on the right side of the world.<br></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"> Press GO to watch the molecules move about the world as they achieve equilibrium. The plot tracks the relative concentrations of each color molecule on each side of the central divider. If the red line dips below 0, there are more red molecules on the left side of the divider than on the right. If it rises above 0, there are more red molecules on the right side of the divider than on the left. The blue line plots the same relationship for blue molecules.<br></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"> You can add more red molecules to the right side of the world by pressing ADD RED.<br></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"> Similarly, you can shrink or expand the right side of the box with the buttons SHRINK RIGHT and EXPAND RIGHT, respectively.<br></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"> Finally, to change the size of the connection window, move the WINDOW slider to your desired size and then press the CHANGE WINDOW button.<br></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"> </p></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"> </del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"> </del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"> <h2>Things to Notice</h2></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"> <p style="text-align:justify"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"> Pay attention to the plot and compare it what you see in the world. Is there an equal number of blue and red molecules on each side of the divider according to the plot and according to what you see in the view?</p></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"> <h2>Things to Try</h2></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"> <p style="text-align:justify"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"> Run the model with several different states for each variable. Do you observe similar equilibrium effects to those seen in Simple Kinetics 2? Are there significant differences?<br></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"> Does the temperature affect the system in the same way it affected the chemical reaction in Simple Kinetics 2? Why or why not?<br></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"> How does changing the concentration affect the rate at which the molecules achieve equilibrium? Does this make sense?<br></p></del></div></td><td colspan="2"> </td></tr>
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</table>Kyleharrisonhttp://2013.igem.org/wiki/index.php?title=Team:Dundee/Project/NetlogoSec&diff=258926&oldid=prevKyleharrison at 11:27, 1 October 20132013-10-01T11:27:55Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> value="<del class="diffchange diffchange-inline">SECGATEcoloursprobabilities</del>.nlogo"></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> value="<ins class="diffchange diffchange-inline">SECGATEcommented</ins>.nlogo"></div></td></tr>
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</table>Kyleharrisonhttp://2013.igem.org/wiki/index.php?title=Team:Dundee/Project/NetlogoSec&diff=258924&oldid=prevKyleharrison at 11:27, 1 October 20132013-10-01T11:27:03Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <applet code="org.nlogo.lite.Applet"</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <applet code="org.nlogo.lite.Applet"</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> codebase="http://www.kyleharrison.co.uk/netlogo/" </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> codebase="http://www.kyleharrison.co.uk<ins class="diffchange diffchange-inline">/igem</ins>/netlogo<ins class="diffchange diffchange-inline">/SecNetlogoApplet</ins>/" </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> archive="NetLogoLite.jar"</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> archive="NetLogoLite.jar"</div></td></tr>
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</table>Kyleharrisonhttp://2013.igem.org/wiki/index.php?title=Team:Dundee/Project/NetlogoSec&diff=254264&oldid=prevKyleharrison: Created page with "{{:Team:Dundee/Templates/Navigationbar}} <html> <html lang="en"> <!-- Begin page content --> <div class="container"> <!-- Title --> <div class="page-..."2013-09-30T14:46:14Z<p>Created page with "{{:Team:Dundee/Templates/Navigationbar}} <html> <html lang="en"> <!-- Begin page content --> <div class="container"> <!-- Title --> <div class="page-..."</p>
<p><b>New page</b></p><div>{{:Team:Dundee/Templates/Navigationbar}}<br />
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<br />
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<h2><b>NetLogo </b> - SECGATE Transportation</h2><br />
<p style="text-align:justify"><br />
The applet requires Java 5 or higher. Java must be enabled in your browser settings. Mac users must have Mac OS X 10.4 or higher. Windows and Linux users may obtain the latest Java from Oracle's Java site.<br />
</p><br />
</div><br />
<!-- Title End --><br />
<br />
<div class="span12" style="margin-left:0px;margin-top: 10px;"><br />
<applet code="org.nlogo.lite.Applet"<br />
codebase="http://www.kyleharrison.co.uk/netlogo/" <br />
archive="NetLogoLite.jar"<br />
width="1330" height="556"><br />
<param name="DefaultModel"<br />
value="SECGATEcoloursprobabilities.nlogo"><br />
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value="-Djnlp.packEnabled=true"><br />
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<br />
<h2>WHAT IS IT?</h2><br />
<p style="text-align:justify"><br />
This model follows on the Simple Kinetics 2 model. In Simple Kinetics 2, we saw how changes to variables such as temperature, volume, and concentration affected the rate at which a chemical reaction reached an equilibrium state. Here we model the same phenomenon based upon a physical separation.<br />
<br />
This model investigates some laboratory methods that chemists use to purify chemicals. Most of these methods are based upon physical properties of molecular separation. The same principles that affect chemical equilibrium affect physical equilibrium as well. By changing the variables of temperature, volume, and concentration, we can affect not only the speed at which a system reaches equilibrium, but also the nature of the distribution ratio. In this model, we watch how these factors affect the physical distribution of red molecules that are considered “dissolved” in a blue solvent.<br />
</p><br />
<br />
<h2>HOW TO USE IT</h2><br />
<p style="text-align:justify"><br />
Setup the model by pressing either the SETUP-RANDOM or the SETUP-SIDE buttons at the top of the Interface tab. SETUP-RANDOM distributes all the molecules randomly around the world. SETUP-SIDE distributes the blue molecules evenly, while placing the red molecules on the right side of the world.<br><br />
<br />
Press GO to watch the molecules move about the world as they achieve equilibrium. The plot tracks the relative concentrations of each color molecule on each side of the central divider. If the red line dips below 0, there are more red molecules on the left side of the divider than on the right. If it rises above 0, there are more red molecules on the right side of the divider than on the left. The blue line plots the same relationship for blue molecules.<br><br />
<br />
You can add more red molecules to the right side of the world by pressing ADD RED.<br><br />
<br />
Similarly, you can shrink or expand the right side of the box with the buttons SHRINK RIGHT and EXPAND RIGHT, respectively.<br><br />
<br />
Finally, to change the size of the connection window, move the WINDOW slider to your desired size and then press the CHANGE WINDOW button.<br><br />
</p><br />
<br />
<br />
<h2>Things to Notice</h2><br />
<p style="text-align:justify"><br />
Pay attention to the plot and compare it what you see in the world. Is there an equal number of blue and red molecules on each side of the divider according to the plot and according to what you see in the view?</p><br />
<br />
<h2>Things to Try</h2><br />
<p style="text-align:justify"><br />
Run the model with several different states for each variable. Do you observe similar equilibrium effects to those seen in Simple Kinetics 2? Are there significant differences?<br><br />
Does the temperature affect the system in the same way it affected the chemical reaction in Simple Kinetics 2? Why or why not?<br><br />
How does changing the concentration affect the rate at which the molecules achieve equilibrium? Does this make sense?<br></p><br />
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